PDBsum entry 2nq6

Hydrolase

PDB id: 2nq6

Contents

Protein chain

304 a.a. *

Ligands

HM4

GOL

Metals

_CO ×3

_CA

Waters ×340

* Residue conservation analysis

PDB id:

2nq6

Name:

Hydrolase

Title:

Crystal structure of human methionine aminopeptidase type 1 in complex with 3-tert-butoxycarbonylaminopyridine-2-carboxylic acid thiazole-2- ylamide

Structure:

Methionine aminopeptidase 1. Chain: a. Fragment: residues 81-384. Synonym: metap 1. Map 1. Peptidase m 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: metap1, kiaa0094. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.50Å R-factor: 0.173 R-free: 0.204

Authors:

A.Addlagatta,B.W.Matthews

Key ref:

X.Hu et al. (2006). Elucidation of the function of type 1 human methionine aminopeptidase during cell cycle progression. Proc Natl Acad Sci U S A, 103, 18148-18153. PubMed id: 17114291 DOI: 10.1073/pnas.0608389103

Date:

30-Oct-06 Release date: 21-Nov-06

Protein chain

P53582  (MAP11_HUMAN) -  Methionine aminopeptidase 1 from Homo sapiens

Seq: 386 a.a.

Struc: 304 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.11.18 - methionyl aminopeptidase.
• Reaction: Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
• Cofactor: Cobalt cation

DOI no: 10.1073/pnas.0608389103

Proc Natl Acad Sci U S A 103:18148-18153 (2006)

PubMed id: 17114291

Elucidation of the function of type 1 human methionine aminopeptidase during cell cycle progression.

X.Hu, A.Addlagatta, J.Lu, B.W.Matthews, J.O.Liu.

ABSTRACT

Processing of the N-terminal initiator methionine is an essential cellular process conserved from prokaryotes to eukaryotes. The enzymes that remove N-terminal methionine are known as methionine aminopeptidases (MetAPs). Human MetAP2 has been shown to be required for the proliferation of endothelial cells and angiogenesis. The physiological function of MetAP1, however, has remained elusive. In this report we demonstrate that a family of inhibitors with a core structure of pyridine-2-carboxylic acid previously developed for the bacterial and yeast MetAP1 is also specific for human MetAP1 (HsMetAP1), as confirmed by both enzymatic assay and high-resolution x-ray crystallography. Treatment of tumor cell lines with the MetAP1-specific inhibitors led to an accumulation of cells in the G(2)/M phase, suggesting that HsMetAP1 may play an important role in G(2)/M phase transition. Overexpression of HsMetAP1, but not HsMetAP2, conferred resistance of cells to the inhibitors, and the inhibitors caused retention of N-terminal methionine of a known MetAP substrate, suggesting that HsMetAP1 is the cellular target for the inhibitors. In addition, when HsMetAP1 was knocked down by gene-specific siRNA, cells exhibited slower progression during G(2)/M phase, a phenotype similar to cells treated with MetAP1 inhibitors. Importantly, MetAP1 inhibitors were able to induce apoptosis of leukemia cell lines, presumably as a consequence of their interference with the G(2)/M phase checkpoint. Together, these results suggest that MetAP1 plays an important role in G(2)/M phase of the cell cycle and that it may serve as a promising target for the discovery and development of new anticancer agents.

Selected figure(s)

Figure 1.
Fig. 1. Inhibition of MetAP by compound 1. Shown is SDS/PAGE Western blot analysis of HeLa cells exposed to compound 1 at the indicated concentrations for 24 h. The membrane was probed with a monoclonal antibody specific for the methionylated 14-3-3 (Upper) and tubulin (Lower).

Figure 5.
Fig. 5. Crystal structure of truncated HsMetAP1 in complex with 1 and 2. (A) Superposed is the "omit" electron density map shown in the inhibitor binding region of compounds 1 and 2. Coefficients are (F[o] – F[c]), where the F[o] are the observed structure amplitudes. The calculated amplitudes F[c] and phases are obtained from the refined model with the inhibitors removed. The maps calculated are at 1.5 Å (contoured at 3.6 ) for 1 and at 1.6 Å (contoured at 3.6 ) for 2. (B) Stereo diagram showing the superposition of enzyme-inhibitor complexes of compounds 1 (green) and 2 (magenta) in the active site pocket of the truncated HsMetAP1 (cyano). Note that both the compounds use a third metal ion (Co^II) in binding to the protein. Except for the contact through the metal ion, there are no obvious hydrogen bond contacts between the protein and the inhibitors, although they share several hydrophobic interactions. (C) Stereo diagram of the superposed structures of HsMetAP1 in complex with compounds 1 and 2 and HsMetAP2 (silver). Note that Tyr-444 of the latter enzyme experiences a severe steric clash with the side chains of compounds 1 and 2, explaining the lower affinity of these compounds for HsMetAP2.

Figures were selected by an automated process.